Searching journal content for articles similar to DeMare et al. 23 (8): 1224.

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  1. Research: Ultra-long-range interactions between active regulatory elements
    • Elias T. Friman,
    • Ilya M. Flyamer,
    • Davide Marenduzzo,
    • Shelagh Boyle,
    • and Wendy A. Bickmore
    Genome Res. August 2023 33: 1269-1283; Published in Advance July 14, 2023, doi:10.1101/gr.277567.122
    ...associated with enriched chromatin interactions, we performed our analysis on Micro-C data from WT mESCs (Fig. 1C; Supplemental Fig. S2A,B; Supplemental Table S1; Hsieh et al. 2020). Cohesin-associated factors were enriched for interactions at short but not long range, and polycomb-associated factors were...
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  2. Research: An AR-ERG transcriptional signature defined by long-range chromatin interactomes in prostate cancer cells
    • Zhizhuo Zhang,
    • Kern Rei Chng,
    • Shreyas Lingadahalli,
    • Zikai Chen,
    • Mei Hui Liu,
    • Huy Hoang Do,
    • Shaojiang Cai,
    • Nicola Rinaldi,
    • Huay Mei Poh,
    • Guoliang Li,
    • Ying Ying Sung,
    • Charlie L. Heng,
    • Leighton J. Core,
    • Si Kee Tan,
    • Xiaoan Ruan,
    • John T. Lis,
    • Manolis Kellis,
    • Yijun Ruan,
    • Wing-Kin Sung,
    • and Edwin Cheung
    Genome Res. February 2019 29: 223-235; Published in Advance January 3, 2019, doi:10.1101/gr.230243.117
    ...of genomic structural alterations.In this study, utilizing our previously developed genomic technology (Fullwood et al. 2009), chromatin interaction analysis by paired-end tag (ChIA-PET) sequencing, we comprehensively mapped AR- and ERG-associated chromatin loops and characterized in detail their interaction...
  3. Research: Cohesin-based chromatin interactions enable regulated gene expression within preexisting architectural compartments
    • Vlad C. Seitan,
    • Andre J. Faure,
    • Ye Zhan,
    • Rachel Patton McCord,
    • Bryan R. Lajoie,
    • Elizabeth Ing-Simmons,
    • Boris Lenhard,
    • Luca Giorgetti,
    • Edith Heard,
    • Amanda G. Fisher,
    • Paul Flicek,
    • Job Dekker,
    • and Matthias Merkenschlager
    Genome Res. December 2013 23: 2066-2077; Published in Advance September 3, 2013, doi:10.1101/gr.161620.113
    ...cells. In addition, cohesin associates with active enhancers and promoters and with CTCF to form long-range interactions important for gene regulation. Although these findings suggest an important role for cohesin in genome organization, this role has not been assessed on a global scale. Unexpectedly...
  4. Research: Genome-wide map of regulatory interactions in the human genome
    • Nastaran Heidari,
    • Douglas H. Phanstiel,
    • Chao He,
    • Fabian Grubert,
    • Fereshteh Jahanbani,
    • Maya Kasowski,
    • Michael Q. Zhang,
    • and Michael P. Snyder
    Genome Res. December 2014 24: 1905-1917; Published in Advance September 16, 2014, doi:10.1101/gr.176586.114
    ...expression. We generated a genome-wide interaction map of regulatory elements in human cells (ENCODE tier 1 cells, K562, GM12878) using Chromatin Interaction Analysis by Paired-End Tag sequencing (ChIA-PET) experiments targeting six broadly distributed factors. Bound regions covered 80% of DNase I...
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  5. Research: Widespread contribution of transposable elements to the innovation of gene regulatory networks
    • Vasavi Sundaram,
    • Yong Cheng,
    • Zhihai Ma,
    • Daofeng Li,
    • Xiaoyun Xing,
    • Peter Edge,
    • Michael P. Snyder,
    • and Ting Wang
    Genome Res. December 2014 24: 1963-1976; Published in Advance October 15, 2014, doi:10.1101/gr.168872.113
    ...chromatin signatures, including reduced DNA methylation and increased enhancer-associated histone marks. On average, 66% of TE-derived binding events were cell type-specific with a cell type-specific epigenetic landscape. Most of the binding sites contributed by TEs were species-specific, but we also...
  6. Research: Enhancers with tissue-specific activity are enriched in intronic regions
    • Beatrice Borsari,
    • Pablo Villegas-Mirón,
    • Sílvia Pérez-Lluch,
    • Isabel Turpin,
    • Hafid Laayouni,
    • Alba Segarra-Casas,
    • Jaume Bertranpetit,
    • Roderic Guigó,
    • and Sandra Acosta
    Genome Res. August 2021 31: 1325-1336; Published in Advance July 21, 2021, doi:10.1101/gr.270371.120
    ...Beatrice Borsari1,6, Pablo Villegas-Mirón2,6, Sílvia Pérez-Lluch1, Isabel Turpin2, Hafid Laayouni2,3, Alba Segarra-Casas2, Jaume Bertranpetit2, Roderic Guigó1,4 and Sandra Acosta2,5 1Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona 08003, Catalonia...
  7. Research: Functional and topological characteristics of mammalian regulatory domains
    • Orsolya Symmons,
    • Veli Vural Uslu,
    • Taro Tsujimura,
    • Sandra Ruf,
    • Sonya Nassari,
    • Wibke Schwarzer,
    • Laurence Ettwiller,
    • and François Spitz
    Genome Res. March 2014 24: 390-400; Published in Advance January 7, 2014, doi:10.1101/gr.163519.113
    ..., MA 01938, USA Abstract Long-range regulatory interactions play an important role in shaping gene-expression programs. However, the genomic features that organize these activities are still poorly characterized. We conducted a large operational analysis to chart the distribution of gene...
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